exRNAdisease

Entry Detail

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General Information

Database ID: exR0000489 RNA Name: ALDH4A1 RNA Type: mRNA Chromosome: chr1 Starnd: - Coordinate: Start Site(bp): 18871430 End Site(bp): 18902724 External Links: ENSG00000159423

Disease Information

Disease Name: Down Syndrome Disease Category: Congenital, Hereditary, and Neonatal Diseases and Abnormalities MeSH ID: D004314 Type: Diseases Category/Congenital, Hereditary, and Neonatal Diseases and Abnormalities Alias: Syndrome, Down//Mongolism//47,XY,+21//Trisomy G//47,XX,+21//Down's Syndrome//Downs Syndrome//Syndrome, Down's//Trisomy 21//Trisomy 21, Mitotic Nondisjunction//Down Syndrome, Partial Trisomy 21//Partial Trisomy 21 Down Syndrome//Trisomy 21, Meiotic Nondisjunction

Expression Detail

GEO ID: GSE16176 Description: Expression profiles of amniotic fluid from human fetuses with Down syndrome and euploid controls Experimental Design: Disease vs Control Case Disease Type: Down Syndrome Case Disease SubType: NA Case Sample: Down Syndrome Control Sample: Normal Number of Case: 7 Number of Control: 7 Number of Samples: 14

Regulatory Relationship

mRNA targets: Gene Symbol Chromosome Start Site(bp) End Site(bp) Strand DDI2 chr1 15617458 15669044 + LIN28A chr1 26410817 26429728 + EIF5 chr14 103333544 103345025 + RPL7A chr9 133348218 133351426 + SLC39A1 chr1 153959099 153968184 - GRB2 chr17 75318076 75405709 - RPL23 chr17 38847860 38853764 - ERBB2 chr17 39687914 39730426 + CASP7 chr10 113679162 113730907 + METTL16 chr17 2405562 2511891 - SERF2 chr15 43777087 43802589 + ESPL1 chr12 53268299 53293638 + SBF1 chr22 50445000 50475035 - ACTB chr7 5527148 5563784 - OSBPL9 chr1 51577179 51798427 + HLA-DRB1 chr6 32578769 32589848 - EXOSC7 chr3 44975241 45036066 + DCTN1 chr2 74361154 74392087 - HDHD5 chr22 17137511 17165287 - RHNO1 chr12 2876258 2889524 + ZDHHC16 chr10 97446170 97457370 + EIF3H chr8 116642130 116766925 - BCAM chr19 44809071 44821421 + FRAS1 chr4 78057323 78544269 + NKTR chr3 42600655 42648735 + TUBA1A chr12 49184795 49189080 - EEF1B2 chr2 206159585 206162928 + SIGIRR chr11 405716 417455 - FUS chr16 31180110 31194871 + CTNNBIP1 chr1 9848276 9910336 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AD000090.1 chr19 35557956 35581954 + AL022311.1 chr22 37876148 37895563 + LINC01641 chr1 227393554 227431035 + Display:

Experiment Detail

GEO ID: GSE16176 Sample Source: Amniotic Fluid Source Fraction: Supernatant Platform: GPL570 Method: Microarray Num of detected RNA Type: 1 Num of detected RNAs of this Type: 17063 Sample treatment protocol: NA RNA Extract protocol: RNA was extracted from 10 mL AF with 30 mL TRIzol LS Reagent (Invitrogen, Carlsbad, CA) and 8 mL chloroform. After RNA extraction, RNA was purified and DNA was removed using the RNeasy® Maxi Kit, including the DNase step according to the manufacturer's protocol (QIAGEN, Valencia, CA). RNA was precipitated using 3M NaOAc and 100% ethanol, and 80% ethanol was added after 4 hours incubation at -20 °C. cDNA, synthesized from extracted RNA, was amplified and purified using the WT-Ovation™ Pico RNA Amplification System (NuGEN, San Carlos, CA) and the DNA Clean & Concentrator™-25 (Zymo Research, Orange, CA). RNA library preparation protocol: biotin Samples were labeled using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN, San Carlos, CA).

Reference

PMID: 19474297 Title: Functional genomic analysis of amniotic fluid cell-free mRNA suggests that oxidative stress is significant in Down syndrome fetuses Author: Slonim DK, Koide K, Johnson KL, Tantravahi U, Cowan JM, Jarrah Z, Bianchi DW Journal: Proc Natl Acad Sci U S A. 2009 Jun 9;106(23):9425-9. Description: To characterize the differences between second trimester Down syndrome (DS) and euploid fetuses, we used Affymetrix microarrays to compare gene expression in uncultured amniotic fluid supernatant samples.